install.packages('devtools')
Note that whenever the rockyIntertidal package is
updated, you can rerun this code to install the latest version.
library(devtools)
install_github("KateMMiller/rockyIntertidal")
library(rockyIntertidal)
Note that R is not able to connect to files on Sharepoint or MS Teams
(b/c Teams also stores all files on Sharepoint). That means you need to
store data package files on your local machine or on a server (e.g. NETN
Z drive). The default option for importing data will add the data
package views (i.e., flatfiles) to an environment called ROCKY to your
Environment work space (i.e. Environment tab in top right panel). If you
would rather import each individual view into your R session, specify
with the new_env argument (e.g., importData(new_env = F)).
To import data using the default settings (i.e. run
importData() with no arguments), you must have the rocky
intertidal front end set as a User DSN called rocky_FE. The database
front end must also be linked with the latest rocky intertidal backend
to pull in the latest data (see “Setting up DSN” tab for more
details).
Option 1. Import data via .csv files. The file path should be where csvs are on your machine or server.
importData(type = 'csv',
filepath = "C:/NETN/R_Dev/data") # update filepath to your computer
Option 2. Import data via zip file of csvs. The filepath should be the location and name of the zip file.
importData(type = 'zip',
filepath = "C:/NETN/R_Dev/data/NETN_RockyIntertidal_Data_Package_20240927.zip")
Option 3. Import data via data package database file on your computer
importData(type = 'dbfile',
filepath = "C:/NETN/R_Dev/data/NETN_RockyIntertidal_Database_fe_20240919.accdb")
Option 4. Import data via data package database DSN (Data Source Name) on your computer. Note that this is the default setting. As long as you have a named DSN called “rocky_FE” that links to the data package database, and that database links to the latest rocky intertidal backend database, the code below will run. See Setting up DSN tab for how to set up DSN.
importData() # easiest
importData(type = 'DSN', odbc = "rocky_FE") # equivalent to line above
You can export all of the csvs to a zip file with the day’s date stamped on the file name. This allows you to import the tables from the database, then export the csvs as one zip file.
exportData(filepath = "./data", zip = TRUE)
The water temperature data is stored as separate csvs and so has a
different import function and process. The temp logger files will go
into your ROCKY environment named the 6 letter location code. The
buoy = T loads the buoy data for each park to the ROCKY
environment. The simplify = T simplifies the datasets to
include only 1 logger measurement per high tide event (for water temp)
and 1 buoy record per day. All plotting functions require the simplified
data. The latest compiled files are on the Z drive here:
“Z:/PROJECTS/MONITORING/Rocky_Intertidal/NETN/5_Data/Data_Files/Temperature/Compiled_HT_water_temps_2011-2022/”.
This reminds me that I need to update the data to include 2023.
#path = "Z:/PROJECTS/MONITORING/Rocky_Intertidal/NETN/5_Data/Data_Files/Temperature/Compiled_HT_water_temps_2011-2022/"
path = "C:/NETN/R_Dev/data/rocky/temp_data/Compiled_HT_water_temps"
importWaterTemp(path = path, buoy = T, simplify = T)
The functions in the rockyIntertidal package are
designed to work with the views, and are the best way to interact with
the data to query by park, site, site type, year, parameter, etc.
However, if you want to view the raw data, and you imported the data
into the ROCKY environment, you can access them with the code below:
# See list of the views
names(ROCKY)
# View one of the views
View(ROCKY$Bolts)
# See top 6 records
head(ROCKY$Echinoderm_Counts)
# Check structure of view
str(ROCKY$Echinoderm_Counts)
# Assign a view to a data frame named bolts in R. Interact with bolts the way you would work with any normal data frame in R.
bolts <- ROCKY$Bolts
While this works, the better approach is to use the “getter” functions within the R package, which access the same files, but allow you to also query data based on park, location, years, plot name, species, etc. See the specific getter function tabs for details.
If you want to use the print_head() function that shows
output in the markdown, run the code below. This makes the results print
cleaner in the markdown report. For your purposes, you can just run:
head(dataframe).
print_head <- function(df){
knitr::kable(df[1:6,]) |> #, table.attr = "style='width:60%;'") |>
kableExtra::kable_classic(full_width = F, font_size = 12,
bootstrap_options = c("condensed"))
}
If you’re contributing to the package, you’ll need to use build tools to build and install the package to test changes before posting to GitHub. Unfortunately Software Center installs RTools44 in C:/Program Files/, not C:/, which is where RStudio looks for it by default. The following code helps RStudio find RTools. You may occasionally have to rerun this code (except for the usethis line), so keep it handy. You know when you have to rerun the code when you try to rebuild a package, and a window pops up to ask if you want to install missing build files.
# Set r environ to find rtools on opening
usethis::edit_r_environ()
Sys.setenv(PATH = paste("C:\\PROGRA~1\\Rtools44\\bin", Sys.getenv("PATH"), sep=";"))
Sys.setenv(BINPREF = "C:\\PROGRA~1\\Rtools44\\mingw_$(WIN)\\bin\\")
The functions in rockyIntertidal have help documentation
like any R package. To view the help, you can go to the Packages tab and
click on rockyIntertidal (see below). That will show you all the
functions in the package. Clicking on individual functions will take you
to the help documentation for that function.
You can also see the help of a function by running, for example:
?importData
If rockyIntertidal isn’t loaded yet, you’d run:
?rockyIntertidal::importData
Each function’s help includes a Description, Usage (i.e. function arguments and their defaults), Argument options/definitions, and several examples showing how the function can be used.
This is where you come in! If you notice typos or can think of better descriptions, examples, error messages, etc., please send them my way! After we’re more comfortable with R packages and get versed on GitHub, you’ll be able to make those changes directly in the package. For now, you can just send me your suggestions and I’ll make the changes.
Finally, if you ever want to peak under the hood at the function, you can view it several ways.View code in the GitHub katemmiller/rockyIntertidal repo. The functions are in the R folder.
Get bolt data for ACAD barnacle recruitment plots
print_head(getBolts(park = "ACAD", plotType = "Recruitment Plot"))
| GroupCode | GroupName | UnitCode | UnitName | SiteName | SiteCode | Label | PlotName | PlotType | CommunityType | BoltLatitude | BoltLongitude | LatLong_Datum | Bolt_UTM_E | Bolt_UTM_N | Bolt_UTM_Zone | Bolt_UTM_Datum | Bolt_NAVD88_Elev | Bolt_MLLW_Elev | Notes | IsBoltCUI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | Bass Harbor | BASHAR | S1 bolt 01 | S1 | Recruitment Plot | Barnacle | 44.22448 | -68.32216 | WGS84 | 554148.7 | 4897066 | 19 | NAD83 | 0.453275 | 2.274275 | NA | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | Bass Harbor | BASHAR | S1 bolt 02 | S1 | Recruitment Plot | Barnacle | 44.22448 | -68.32215 | WGS84 | 554148.7 | 4897066 | 19 | NAD83 | 0.475296 | 2.296296 | NA | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | Bass Harbor | BASHAR | S1 label | S1 | Recruitment Plot | Barnacle | 44.22448 | -68.32216 | WGS84 | 554148.7 | 4897066 | 19 | NAD83 | 0.429081 | 2.250081 | NA | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | Bass Harbor | BASHAR | S2 bolt 01 | S2 | Recruitment Plot | Barnacle | 44.22446 | -68.32218 | WGS84 | 554148.7 | 4897066 | 19 | NAD83 | 0.431997 | 2.252997 | NA | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | Bass Harbor | BASHAR | S2 bolt 02 | S2 | Recruitment Plot | Barnacle | 44.22446 | -68.32218 | WGS84 | 554148.7 | 4897066 | 19 | NAD83 | 0.409523 | 2.230523 | NA | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | Bass Harbor | BASHAR | S2 label | S2 | Recruitment Plot | Barnacle | 44.22446 | -68.32218 | WGS84 | 554148.7 | 4897066 | 19 | NAD83 | 0.405884 | 2.226884 | NA | FALSE |
Get bolt data for Calf Island photoplots
print_head(getBolts(site = "CALISL", plotType = "Photoplot"))
| GroupCode | GroupName | UnitCode | UnitName | SiteName | SiteCode | Label | PlotName | PlotType | CommunityType | BoltLatitude | BoltLongitude | LatLong_Datum | Bolt_UTM_E | Bolt_UTM_N | Bolt_UTM_Zone | Bolt_UTM_Datum | Bolt_NAVD88_Elev | Bolt_MLLW_Elev | Notes | IsBoltCUI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | BOHA | Boston Harbor Islands National Park Area | Calf Island | CALISL | A1 bolt 01 | A1 | Photoplot | Ascophyllum | 42.34241 | -70.89479 | WGS84 | 343821.4 | 4689574 | 19 | NAD83 | 0.107605 | 1.785605 | NA | FALSE |
| NETN | Northeast Temperate Network | BOHA | Boston Harbor Islands National Park Area | Calf Island | CALISL | A1 bolt 02 | A1 | Photoplot | Ascophyllum | 42.34241 | -70.89478 | WGS84 | 343821.4 | 4689574 | 19 | NAD83 | -0.063546 | 1.614454 | NA | FALSE |
| NETN | Northeast Temperate Network | BOHA | Boston Harbor Islands National Park Area | Calf Island | CALISL | A1 bolt 03 | A1 | Photoplot | Ascophyllum | 42.34241 | -70.89478 | WGS84 | 343821.4 | 4689574 | 19 | NAD83 | -0.140115 | 1.537885 | NA | FALSE |
| NETN | Northeast Temperate Network | BOHA | Boston Harbor Islands National Park Area | Calf Island | CALISL | A1 bolt 04 | A1 | Photoplot | Ascophyllum | 42.34242 | -70.89478 | WGS84 | 343821.4 | 4689574 | 19 | NAD83 | -0.107108 | 1.570892 | NA | FALSE |
| NETN | Northeast Temperate Network | BOHA | Boston Harbor Islands National Park Area | Calf Island | CALISL | A1 label | A1 | Photoplot | Ascophyllum | 42.34241 | -70.89479 | WGS84 | 343821.4 | 4689574 | 19 | NAD83 | 0.095710 | 1.773710 | NA | FALSE |
| NETN | Northeast Temperate Network | BOHA | Boston Harbor Islands National Park Area | Calf Island | CALISL | A2 bolt 01 | A2 | Photoplot | Ascophyllum | 42.34242 | -70.89481 | WGS84 | 343821.4 | 4689574 | 19 | NAD83 | 0.249903 | 1.927903 | NA | FALSE |
Default filter returns all summer records except QAQC records and blank counts.
print_head(getBarnacleRecruitment())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | QAQCType | PlotName | Count | Notes | DateScored | Scorer | IsPointCUI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | S1 | 708 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | S2 | 458 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | S3 | 170 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | S4 | 145 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | S5 | 390 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | U1 | 368 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
Barnacle counts for ACAD only sites
print_head(getBarnacleRecruitment(park = "ACAD"))
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | QAQCType | PlotName | Count | Notes | DateScored | Scorer | IsPointCUI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | S1 | 708 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | S2 | 458 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | S3 | 170 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | S4 | 145 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | S5 | 390 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | NA | U1 | 368 | Scoring date not known. | NA | {DB5AAE5D-8B53-4EAF-8DA9-43E7ABB19099} | FALSE |
Barnacle counts for different combinations of parks, sites, plots, and years
barn_sumwin <- getBarnacleRecruitment(park = "ACAD", plotName = "all") # summer and winter counts
barn_BOHA <- getBarnacleRecruitment(park = "BOHA")
barn_5yr <- getBarnacleRecruitment(years = 2016:2021)
barn_first_last <- getBarnacleRecruitment(years = c(2013, 2021))
barn24_qaqc <- getBarnacleRecruitment(years = 2024, QAQC = TRUE)
barn_na <- getBarnacleRecruitment(dropNA = F) # returns NA records too
Note that the getter functions only return the raw data from the
views. Elevation is calculated in sumPISpecies()
Default returns all records except QAQC visits and blank distances
print_head(getPIBoltDistance())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | PlotName | Label | Elevation_MLLW_m | Distance_m | IsPointCUI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia NP | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | T1 | T1 bolt 01 | 3.487006 | 0.00 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia NP | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | T1 | T1 bolt 02 | 3.184000 | 1.04 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia NP | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | T1 | T1 bolt 03 | NA | 1.53 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia NP | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | T1 | T1 bolt 04 | 2.668736 | 3.16 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia NP | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | T1 | T1 bolt 05 | 2.543000 | 3.89 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia NP | SCHPOI | Schoodic Point | 2013-06-19 | 2013 | FALSE | T1 | T1 bolt 06 | 2.958020 | 4.95 | FALSE |
PI Bolt distances for different combinations of parks, sites, plots, and years
bolt_na <- getPIBoltDistance(dropNA = F) # return NA records too
bolt_t3 <- getPIBoltDistance(park = "ACAD", plotName = "T3")
bolt_BOHA2 <- getPIBoltDistance(site = c("CALISL", "GREISL"))
bolt_5yr <- getPIBoltDistance(years = 2016:2021)
bolt_first_last <- getPIBoltDistance(years = c(2013, 2021))
bolt_with_qaqc <- getPIBoltDistance(years = 2021, QAQC = TRUE)
Default returns all records except QAQC visits and blank Cover values
print_head(getPhotoCover())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | QAQCType | PlotName | CommunityType | BoltLatitude | BoltLongitude | Bolt_UTM_E | Bolt_UTM_N | Bolt_MLLW_Elev | CoverType | ScientificName | CoverCode | PercentCover | Notes | DateScored | Scorer | IsPointCUI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | NA | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Other Algae - Red | Rhodophyta | ALGRED | 0 | NA | 2013-09-03 | {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | NA | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Articulated corallines | Corallinales officinalis | ARTCOR | 0 | NA | 2013-09-03 | {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | NA | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Other Invertebrate | Animalia | OTHINV | 0 | NA | 2013-09-03 | {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | NA | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Laver | Porphyra | PORSPP | 0 | NA | 2013-09-03 | {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | NA | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Unidentified | NA | UNIDEN | 0 | NA | 2013-09-03 | {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | NA | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Tar | NA | TAR | 0 | NA | 2013-09-03 | {1EE29925-05EE-4AEF-967C-2F4D5C2A4724} | FALSE |
Photoplot cover for different combinations of parks, sites, plots, years, etc.
cov_na <- getPhotoCover(dropNA = F) # returns NA records too
cov_a1 <- getPhotoCover(park = "ACAD", plotName = "A1")
cov_BOHA2 <- getPhotoCover(site = c("CALISL", "GREISL"))
cov_ab <- getPhotoCover(park = "BOHA", species = c("ALGBRO"))
cov_5yr <- getPhotoCover(years = 2016:2021)
cov_first_last <- getPhotoCover(years = c(2013, 2021))
cov21_with_qaqc <- getPhotoCover(years = 2021, QAQC = TRUE)
Default returns all records except QAQC visits and blank counts
print_head(getMotileInvertCounts())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | PlotName | CommunityType | BoltLatitude | BoltLongitude | Bolt_UTM_E | Bolt_UTM_N | Bolt_MLLW_Elev | ScientificName | CommonName | SpeciesCode | Damage | No.Damage | Subsampled | IsPointCUI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Littorina littorea | Common periwinkle | LITLIT | 0 | 3 | No | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Littorina obtusata | Smooth periwinkle | LITOBT | 0 | 6 | No | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Littorina saxatilis | Rough periwinkle | LITSAX | 0 | 0 | No | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Nucella lapillus | Dogwhelk | NUCLAP | 0 | 0 | No | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Testudinalia testudinalis | Limpet | TECTES | 0 | 0 | No | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | A1 | Ascophyllum | 44.22468 | -68.32274 | 554148.7 | 4897066 | 2.786703 | Littorina littorea | Common periwinkle | LITLIT | 0 | 2 | No | FALSE |
Motile Invertebrate counts for different combinations of parks, sites, plots, years, etc.
minv_acad <- getMotileInvertCounts(dropNA = F) # return NA counts too
minv_r <- getMotileInvertCounts(park = "ACAD", plotName = c("R1", "R2", "R3", "R4", "R5"))
minv_BOHA2 <- getMotileInvertCounts(site = c("CALISL", "GREISL"))
minv_lit <- getMotileInvertCounts(species = c("LITLIT", "LITOBT", "LITSAX"))
minv_5yr <- getMotileInvertCounts(years = 2016:2021)
minv_first_last <- getMotileInvertCounts(years = c(2013, 2021))
minv21_qaqc <- getMotileInvertCounts(years = 2021, QAQC = TRUE)
Default returns all records except QAQC visits and blank counts
print_head(getMotileInvertMeas())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | PlotName | CommunityType | ScientificName | CommonName | SpeciesCode | Measurement | IsPointCUI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | Littorina littorea | Common periwinkle | LITLIT | 9 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | Littorina littorea | Common periwinkle | LITLIT | 23 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | Littorina obtusata | Smooth periwinkle | LITOBT | 12 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | Littorina obtusata | Smooth periwinkle | LITOBT | 11 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | Littorina obtusata | Smooth periwinkle | LITOBT | 12 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | A1 | Ascophyllum | Littorina obtusata | Smooth periwinkle | LITOBT | 12 | FALSE |
Motile Invertebrate measurements for different combinations of parks, sites, plots, years, etc.
minv_acad <- getMotileInvertMeas(park = "ACAD", dropNA = F) # include NA measurements too
minv_r <- getMotileInvertMeas(park = "ACAD", plotName = c("R1", "R2", "R3", "R4", "R5"))
minv_BOHA2 <- getMotileInvertMeas(site = c("CALISL", "GREISL"))
minv_lit <- getMotileInvertMeas(species = c("LITLIT", "LITOBT", "LITSAX"))
minv_5yr <- getMotileInvertMeas(years = 2016:2021)
minv_first_last <- getMotileInvertMeas(years = c(2013, 2021))
minv21_qaqc <- getMotileInvertMeas(years = 2021, QAQC = TRUE)
Default returns all records except QAQC visits and blank counts
print_head(getEchinoCounts())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | PlotName | ScientificName | SpeciesCode | Count | IsPointCUI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2021-07-18 | 2021 | FALSE | X1 | Asterias forbesi | ASTFOR | 0 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2021-07-18 | 2021 | FALSE | X1 | Strongylocentrotus droebachiensis | STRDRO | 0 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2021-07-18 | 2021 | FALSE | X1 | Asterias rubens | ASTRUB | 0 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2021-07-18 | 2021 | FALSE | X1 | Henricia sanguinolenta | HENSAN | 0 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2024-06-29 | 2024 | FALSE | X1 | Henricia sanguinolenta | HENSAN | 0 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2024-06-29 | 2024 | FALSE | X1 | Asterias rubens | ASTRUB | 0 | FALSE |
Echinoderm counts for different combinations of parks, sites, plots, years, etc.
ech_acad <- getEchinoCounts(park = "ACAD", dropNA = F) # return NA counts too
ech_t3 <- getEchinoCounts(park = "ACAD", plotName = "X3")
ech_BOHA2 <- getEchinoCounts(site = c("CALISL", "GREISL"))
ech_5yr <- getEchinoCounts(years = 2016:2021)
ech_first_last <- getEchinoCounts(years = c(2013, 2021))
ech21_qaqc <- getEchinoCounts(years = 2021, QAQC = TRUE)
Default returns all records except QAQC visits and blank measurements
print_head(getEchinoMeas())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | PlotName | ScientificName | CommonName | SpeciesCode | Measurement | IsPointCUI |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | X2 | Asterias rubens | Common sea star | ASTRUB | 15 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | X2 | Strongylocentrotus droebachiensis | Green sea urchin | STRDRO | 33 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | X2 | Strongylocentrotus droebachiensis | Green sea urchin | STRDRO | 28 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | X2 | Strongylocentrotus droebachiensis | Green sea urchin | STRDRO | 18 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | X2 | Strongylocentrotus droebachiensis | Green sea urchin | STRDRO | 48 | FALSE |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | X2 | Strongylocentrotus droebachiensis | Green sea urchin | STRDRO | 21 | FALSE |
Echinoderm measurements for different combinations of parks, sites, years, etc.
ech_acad <- getEchinoMeas(park = "ACAD", dropNA = F) #returns NAs too
ech_t3 <- getEchinoMeas(park = "ACAD", plotName = "X3")
ech_BOHA2 <- getEchinoMeas(site = c("CALISL", "GREISL"))
ech_5yr <- getEchinoMeas(years = 2016:2021)
ech_first_last <- getEchinoMeas(years = c(2013, 2021))
ech21_qaqc <- getEchinoMeas(years = 2021, QAQC = TRUE)
ech21_ASTFOR <- getEchinoMeas(species = "ASTFOR")
For every get function, there’s a sum function that summarizes the data. This is typically at the site level for a given species and year. For example, averaging across the 3 point intercept transects, or averaging percent cover across the 5 barnacle photoplots. Summary functions are demonstrated below.
The barnacle recruitment summary function calculates the median, min and max of counts for a given plot type (ie summer or winter) for each visit. If there are multiple records for a given site x visit x plot type, you will receive a warning in the console with a description of how the duplicates were handled by the function.
Summarize defaults, which is all parks, all sites, all years, all species, summer-only, non-QAQC visits/QAQC types, and complete records.
print_head(sumBarnacleRecruitment())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | QAQCType | plot_type | median_count | max_count | min_count | num_plots |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | NA | summer | 1260 | 1383 | 1080 | 5 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | NA | winter | 1148 | 1247 | 883 | 5 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | NA | summer | 1333 | 1430 | 972 | 5 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | NA | winter | 573 | 914 | 0 | 5 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2015-06-12 | 2015 | FALSE | NA | summer | 1760 | 2249 | 1722 | 5 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2015-06-12 | 2015 | FALSE | NA | winter | 1256 | 1707 | 780 | 5 |
Summarize different combinations of parks, sites, years, species, etc.
barn_acad <- sumBarnacleRecruitment(park = "ACAD")
barn_summer <- sumBarnacleRecruitment(park = "ACAD", plotName = "summer")
barn_BOHA <- sumBarnacleRecruitment(site = c("CALISL", "GREISL"))
barn_5yr <- sumBarnacleRecruitment(years = 2016:2021)
barn_first_last <- sumBarnacleRecruitment(years = c(2013, 2021))
barn21_qaqc <- sumBarnacleRecruitment(years = 2024, QAQC = TRUE)
This is the function where elevation is calculated for point intercept distances along the transects. Note: you will get a warning if there are impossible distance/elevation combinations in the console and an object called bolt_checks will show up in your workspace environment.
Summarize defaults, which is all parks, all sites, all years, all species, non-QAQC visits, and complete records.
print_head(sumPISpecies())
| UnitCode | SiteCode | SiteName | StartDate | QAQC | Year | PlotName | Label | CoverType | CoverCode | Elevation_MLLW_m | elev_first | elev_last | elev_change | Distance_m | PI_Distance | PI_Elevation |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ACAD | BASHAR | Bass Harbor | 2013-06-21 | FALSE | 2013 | T1 | T1 bolt 01 | Rock | ROCK | 4.51103 | 4.51103 | 4.317431 | 0.1935992 | 0 | 0.0 | 4.511030 |
| ACAD | BASHAR | Bass Harbor | 2013-06-21 | FALSE | 2013 | T1 | T1 bolt 01 | Rock | ROCK | 4.51103 | 4.51103 | 4.317431 | 0.1935992 | 0 | 0.3 | 4.486524 |
| ACAD | BASHAR | Bass Harbor | 2013-06-21 | FALSE | 2013 | T1 | T1 bolt 01 | Water | WATER | 4.51103 | 4.51103 | 4.317431 | 0.1935992 | 0 | 0.6 | 4.462018 |
| ACAD | BASHAR | Bass Harbor | 2013-06-21 | FALSE | 2013 | T1 | T1 bolt 01 | Rock | ROCK | 4.51103 | 4.51103 | 4.317431 | 0.1935992 | 0 | 0.9 | 4.437512 |
| ACAD | BASHAR | Bass Harbor | 2013-06-21 | FALSE | 2013 | T1 | T1 bolt 01 | Rock | ROCK | 4.51103 | 4.51103 | 4.317431 | 0.1935992 | 0 | 1.2 | 4.413005 |
| ACAD | BASHAR | Bass Harbor | 2013-06-21 | FALSE | 2013 | T1 | T1 bolt 01 | Rock | ROCK | 4.51103 | 4.51103 | 4.317431 | 0.1935992 | 0 | 1.5 | 4.388499 |
Summarize different combinations of parks, sites, years, species, etc.
spp_ACAD <- sumPISpecies(park = "ACAD")
spp_t3 <- sumPISpecies(park = "ACAD", plotName = "T3")
spp_BOHA2 <- sumPISpecies(site = c("CALISL", "GREISL"))
spp_fuc <- sumPISpecies(park = "BOHA", species = c("FUCEPI", "FUCSPP"))
spp_5yr <- sumPISpecies(years = 2016:2021)
spp_first_last <- sumPISpecies(years = c(2013, 2021))
spp21_with_qaqc <- sumPISpecies(years = 2021, QAQC = TRUE)
spp_no_drops <- sumPISpecies(drop_missing = FALSE)
Summarize defaults, which is all parks, all sites, all plots, all species, all categories, all communities, non-QAQC visits, and complete records.
print_head(sumPhotoCover())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | CommunityType | CoverType | ScientificName | CoverCode | avg_cover | median_cover | min_cover | max_cover | q25_cover | q75_cover |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Articulated corallines | Corallinales officinalis | ARTCOR | 0.0 | 0 | 0 | 0 | 0 | 0 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Ascophyllum epibiont | Vertebrata lanosa/Elachista fucicola | ASCEPI | 17.6 | 22 | 2 | 27 | 14 | 23 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Barnacle | Semibalanus balanoides | BARSPP | 0.4 | 0 | 0 | 1 | 0 | 1 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Crustose coralline | Phymatolithon lenormandii | CRUCOR | 0.0 | 0 | 0 | 0 | 0 | 0 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Crustose non-coralline | Calothrix | NONCOR | 0.0 | 0 | 0 | 0 | 0 | 0 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Dulse | Palmaria palmata | PALPAL | 0.0 | 0 | 0 | 0 | 0 | 0 |
Summarize different combinations of parks, sites, years, species, etc.
cov_ACAD <- sumPhotoCover(park = "ACAD")
cov_t3 <- sumPhotoCover(park = "ACAD", plotName = "A3")
cov_BOHA2 <- sumPhotoCover(site = c("CALISL", "GREISL"))
cov_ab <- sumPhotoCover(park = "BOHA", species = c("ALGBRO"))
cov_5yr <- sumPhotoCover(years = 2016:2021)
cov23_with_qaqc <- sumPhotoCover(site = "SHIHAR", years = 2023, QAQC = TRUE)
This function summarizes site-level average, median, min and max counts by park, site, plot name, and species.
Summarize defaults, which is all parks, all sites, all plots, all species, all communities, non-QAQC visits, and complete records.
print_head(sumMotileInvertCounts())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | CommunityType | SpeciesCode | ScientificName | CommonName | count_total | count_med | count_avg | count_min | count_max | count_l25 | count_u75 | damaged_total | damaged_med | damaged_avg | damaged_min | damaged_max | damaged_l25 | damaged_u75 | notdamaged_total | notdamaged_med | notdamaged_avg | notdamaged_min | notdamaged_max | notdamaged_l25 | notdamaged_u75 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | LITLIT | Littorina littorea | Common periwinkle | 70 | 16 | 14.0 | 3 | 23 | 8 | 20 | 1 | 0 | 0.2 | 0 | 1 | 0 | 0 | 69 | 16 | 13.8 | 3 | 22 | 8 | 20 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | LITOBT | Littorina obtusata | Smooth periwinkle | 95 | 23 | 19.0 | 6 | 34 | 7 | 25 | 1 | 0 | 0.2 | 0 | 1 | 0 | 0 | 94 | 23 | 18.8 | 6 | 34 | 6 | 25 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | LITSAX | Littorina saxatilis | Rough periwinkle | 0 | 0 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 | 0 | 0 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | NUCLAP | Nucella lapillus | Dogwhelk | 3 | 0 | 0.6 | 0 | 2 | 0 | 1 | 0 | 0 | 0.0 | 0 | 0 | 0 | 0 | 3 | 0 | 0.6 | 0 | 2 | 0 | 1 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | TECTES | Testudinalia testudinalis | Limpet | 0 | 0 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 | 0 | 0 | 0 | 0 | 0.0 | 0 | 0 | 0 | 0 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Barnacle | LITLIT | Littorina littorea | Common periwinkle | 2 | 0 | 0.4 | 0 | 1 | 0 | 1 | 0 | 0 | 0.0 | 0 | 0 | 0 | 0 | 2 | 0 | 0.4 | 0 | 1 | 0 | 1 |
Summarize different combinations of parks, sites, years, species, etc.
cnts_acad <- sumMotileInvertCounts (park = "ACAD")
cnt_a1 <- sumMotileInvertCounts (park = "ACAD", plotName = "A1")
cnt_BOHA2 <- sumMotileInvertCounts (site = c("CALISL", "GREISL"))
cnt_gc <- sumMotileInvertCounts (park = "BOHA", species = c("CARMAE"))
cnt_5yr <- sumMotileInvertCounts (years = 2016:2021)
cnt_first_last <- sumMotileInvertCounts (years = c(2013, 2021))
cnt21_with_qaqc <- sumMotileInvertCounts (years = 2021, QAQC = TRUE)
Summarize defaults, which is all parks, all sites, all plots, all species, all communities, non-QAQC visits, and complete records.
print_head(sumMotileInvertMeas())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | CommunityType | ScientificName | CommonName | SpeciesCode | Meas_5mm_fac | num_meas |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Littorina littorea | Common periwinkle | LITLIT | 5 to 9.9 | 3 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Littorina littorea | Common periwinkle | LITLIT | 10 to 14.9 | 3 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Littorina littorea | Common periwinkle | LITLIT | 15 to 19.9 | 23 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Littorina littorea | Common periwinkle | LITLIT | 20 to 24.9 | 12 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Littorina obtusata | Smooth periwinkle | LITOBT | 5 to 9.9 | 8 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | Ascophyllum | Littorina obtusata | Smooth periwinkle | LITOBT | 10 to 14.9 | 35 |
Summarize different combinations of parks, sites, years, species, etc.
minv_acad <- sumMotileInvertMeas(park = "ACAD")
minv_r <- sumMotileInvertMeas(park = "ACAD", plotName = c("R1", "R2", "R3", "R4", "R5"))
minv_BOHA2 <- sumMotileInvertMeas(site = c("CALISL", "GREISL"))
minv_lit <- sumMotileInvertMeas(species = c("LITLIT", "LITOBT", "LITSAX"))
minv_5yr <- sumMotileInvertMeas(years = 2016:2021)
minv_first_last <- sumMotileInvertMeas(years = c(2013, 2021))
minv21_qaqc <- sumMotileInvertMeas(years = 2021, QAQC = TRUE)
This function summarizes site-level average, median, min and max counts by park, site, plot name, and species.
Summarize defaults, which is all parks, all sites, all plots, all species, non-QAQC visits, and complete records.
print_head(sumEchinoCounts())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | SpeciesCode | ScientificName | count_total | count_med | count_avg | count_min | count_max | count_l25 | count_u75 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | ASTFOR | Asterias forbesi | 0 | 0 | 0.0000000 | 0 | 0 | 0 | 0.0 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | ASTRUB | Asterias rubens | 0 | 0 | 0.0000000 | 0 | 0 | 0 | 0.0 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | HENSAN | Henricia sanguinolenta | 0 | 0 | 0.0000000 | 0 | 0 | 0 | 0.0 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2013-06-21 | 2013 | FALSE | STRDRO | Strongylocentrotus droebachiensis | 0 | 0 | 0.0000000 | 0 | 0 | 0 | 0.0 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | ASTFOR | Asterias forbesi | 0 | 0 | 0.0000000 | 0 | 0 | 0 | 0.0 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | ASTRUB | Asterias rubens | 1 | 0 | 0.3333333 | 0 | 1 | 0 | 0.5 |
Summarize different combinations of parks, sites, years, species, etc.
cnts_ACAD <- sumEchinoCounts (park = "ACAD")
cnt_a1 <- sumEchinoCounts (park = "ACAD", plotName = "X1")
cnt_BOHA2 <- sumEchinoCounts (site = c("CALISL", "GREISL"))
cnt_af <- sumEchinoCounts (park = "BOHA", species = c("ASTFOR"))
cnt_5yr <- sumEchinoCounts (years = 2016:2021)
cnt_first_last <- sumEchinoCounts (years = c(2013, 2021))
cnt21_with_qaqc <- sumEchinoCounts (years = 2021, QAQC = TRUE)
This function summarizes number of individuals in each 5 mm size class by park, site, and species.
Summarize defaults, which is all parks, all sites, all plots, all species, non-QAQC visits, and complete records.
print_head(sumEchinoMeas())
| GroupCode | GroupName | UnitCode | UnitName | SiteCode | SiteName | StartDate | Year | QAQC | ScientificName | CommonName | SpeciesCode | Meas_5mm_fac | num_meas |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | Asterias rubens | Common sea star | ASTRUB | 15 to 19.9 | 1 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | Strongylocentrotus droebachiensis | Green sea urchin | STRDRO | 15 to 19.9 | 1 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | Strongylocentrotus droebachiensis | Green sea urchin | STRDRO | 20 to 24.9 | 1 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | Strongylocentrotus droebachiensis | Green sea urchin | STRDRO | 25 to 29.9 | 3 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | Strongylocentrotus droebachiensis | Green sea urchin | STRDRO | 30 to 34.9 | 2 |
| NETN | Northeast Temperate Network | ACAD | Acadia National Park | BASHAR | Bass Harbor | 2014-06-21 | 2014 | FALSE | Strongylocentrotus droebachiensis | Green sea urchin | STRDRO | 45 to 49.9 | 1 |
Summarize different combinations of parks, sites, years, species, etc.
minv_acad <- sumEchinoMeas(park = "ACAD")
minv_r <- sumEchinoMeas(park = "ACAD", plotName = c("X1", "X2"))
minv_BOHA2 <- sumEchinoMeas(site = c("CALISL", "GREISL"))
minv_lit <- sumEchinoMeas(species = c("ASTFOR", "ASTRUB"))
minv_5yr <- sumEchinoMeas(years = 2016:2021)
minv_first_last <- sumEchinoMeas(years = c(2013, 2021))
minv21_qaqc <- sumEchinoMeas(years = 2021, QAQC = TRUE)
For most getter and summary functions, there are plotting functions with the same suffix. Some examples are below. See also the examples in the help files for each function.
This function plots median barnacle recruitment counts across the five summer plots per site and year, with error bars representing min and max counts among the five plots. If only 1 plot is specified, then the raw counts will be plotted. If both summer and winter plots are specified, resulting plot will be color-coded by season. If more than one site and year is specified, results will be faceted by site. Note that you will receive a warning if there are duplicate count records for a given site, plot name, and visit.
Plot summer recruitment for all years faceted on ACAD sites
plotBarnacleRecruitment(park = 'ACAD')
These plots combine the point intercept data (dots and symbols on the graph) and the photoplot cover data (pie charts) to compare changes across years.
plotSpeciesContours(site = "BASHAR", years = 2013:2018)
## TableGrob (1 x 2) "arrange": 2 grobs
## z
## 1 1
## 2 2
## cells
## 1 (1-1,1-1)
## 2 (1-1,2-2)
## name
## 1 arrange
## 2 arrange
## grob
## 1 gtable[layout]
## 2 gtable[layout]
Plot the transect contours faceted on transect number
plotPITransects(site = "SHIHAR", years = 2013:2019)
Plot point intercept species detections summarized as median and middle 50% distribution of elevation. There are a lot of arguments to produce different plots and figures. Some of the ones I find most useful are below. Note when years aren’t specified, all years are included by default.
plotPISpecies(site = "BASHAR", facet = T, main_groups = T, plotly = T)
plotPISpecies(park = "BOHA", facet = T, main_groups = T)
plotPISpecies(site = "SHIHAR", rev_axis = T, facet = T)
plotPISpecies(site = "OTTPOI", species = c("FUCSPP", "ASCNOD"), plotly = T)
Plots the photoplot cover summarized as median cover and middle 50% distribution of cover across the photoplots within a target species. Note that there are a lot of arguments that produce different plots and figures (all explained in the help). Here are a few I tend to use the most.
plotPhotoCover(park = "ACAD", community = "Barnacle", plotly = T)
plotPhotoCover(site = "LITHUN", main_groups = T)
plotPhotoCover(site = "LITHUN", top_spp = 3)
plotPhotoCover(site = "LITHUN", top_spp = 3, plotly = T, xlab = NULL, plot_title = "Little Hunter")
plotPhotoCover(site = "LITHUN", main_groups = T, community = "Fucus", plotly = T)
plotPhotoCover(site = "BASHAR", main_groups = T, heatmap = TRUE)
plotMotileInvertCounts(site = "OUTBRE", years = 2013:2021)
plotMotileInvertCounts(site = "OUTBRE", years = 2013:2021, plotly = T)
plotMotileInvertMeas(site = "SHIHAR", years = 2013:2019)
plotEchinoCounts(site = "OUTBRE", years = 2013:2021)
plotEchinoCounts(site = "OUTBRE", years = 2013:2021, plotly = T)
plotEchinoMeas(site = "SHIHAR", years = 2013:2019)
Note the data and functions have not been checked recently, and may not be fully functional
plotWaterTemp(park = "ACAD", years = 2022, facet_col = 1)
plotWaterTemp(site = "BASHAR", years = 2011:2022)
plotBuoyData(park = "ACAD", metric = 'all')
## TableGrob (2 x 1) "arrange": 2 grobs
## z
## 1 1
## 2 2
## cells
## 1 (1-1,1-1)
## 2 (2-2,1-1)
## name
## 1 arrange
## 2 arrange
## grob
## 1 gtable[layout]
## 2 gtable[layout]
plotBuoyData(park = "ACAD", metric = "temp", year = 2022)
The default ggplot aesthetics are too busy, and require several lines
of code to turn off. For every package, I create a theme that turns
those off and can just be run with the ggplot code. For this package use
theme_rocky() as shown below.
dat <- sumPhotoCover(site = "SHIHAR", community = "Ascophyllum", species = "ASCNOD")
library(ggplot2)
ggplot(dat, aes(x = Year, y = median_cover)) +
geom_point() +
theme_rocky()